Gorgeous mosaic of mitochondrial genes created by horizontal transfer and gene conversion

Proceedings of the National Academy of Sciences of the United States of America

Volumn 107, Issue 50, 2010, Pages 21576-21581

  Hao, Weilong ^a   Richardson, Aaron O ^a,b   Zheng, Yihong ^a,c   Palmer, Jeffrey D ^a  

^a INDIANA UNIVERSITY   (United States)

^b UNIVERSITY OF TORONTO   (Canada)

^c WUHAN UNIVERSITY   (China)

Author keywords

Gene duplication; Recombination

Indexed keywords

ARTICLE; BREATHING; CHLOROPLAST; GENE CONVERSION; GENE EXPRESSION; HORIZONTAL GENE TRANSFER; INTRON; MITOCHONDRIAL GENE; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; RNA SPLICING; SPECIES DIFFERENTIATION;

BACTERIA; BASE SEQUENCE; BIOLOGICAL EVOLUTION; GENE CONVERSION; GENE TRANSFER, HORIZONTAL; GENES, MITOCHONDRIAL; GENES, PLANT; GENETIC SPECIATION; GENOME, BACTERIAL; MOLECULAR SEQUENCE DATA; PHYLOGENY; SEQUENCE ALIGNMENT;

BACTERIA (MICROORGANISMS);

EID: 78650727966     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1016295107     Document Type: Article

References (40)

1. Ochman H, Lawrence JG, Groisman EA (2000) Lateral gene transfer and the nature of bacterial innovation. Nature 405:299-304.
2. Beiko RG, Harlow TJ, Ragan MA (2005) Highways of gene sharing in prokaryotes. Proc Natl Acad Sci USA 102:14332-14337.
3. Keeling PJ, Palmer JD (2008) Horizontal gene transfer in eukaryotic evolution. Nat Rev Genet 9:605-618.
4. Bock R (2010) The give-and-take of DNA: Horizontal gene transfer in plants. Trends Plant Sci 15:11-22.
5. Richardson AO, Palmer JD (2007) Horizontal gene transfer in plants. J Exp Bot 58:1-9.
6. Bergthorsson U, Richardson AO, Young GJ, Goertzen LR, Palmer JD (2004) Massive horizontal transfer of mitochondrial genes from diverse land plant donors to the basal angiosperm Amborella. Proc Natl Acad Sci USA 101:17747-17752.
7. Sanchez-Puerta MV, Cho Y, Mower JP, Alverson AJ, Palmer JD (2008) Frequent, phylogenetically local horizontal transfer of the cox1 group I Intron in flowering plant mitochondria. Mol Biol Evol 25:1762-1777.
8. Bergthorsson U, Adams KL, Thomason B, Palmer JD (2003) Widespread horizontal transfer of mitochondrial genes in flowering plants. Nature 424:197-201.
9. Barkman TJ, et al. (2007) Mitochondrial DNA suggests at least 11 origins of parasitism in angiosperms and reveals genomic chimerism in parasitic plants. BMC Evol Biol 7: 248.
10. Klasson L, et al. (2009) The mosaic genome structure of the Wolbachia wRi strain infecting Drosophila simulans. Proc Natl Acad Sci USA 106:5725-5730.
11. Mau B, Glasner JD, Darling AE, Perna NT (2006) Genome-wide detection and analysis of homologous recombination among sequenced strains of Escherichia coli. Genome Biol 7:R44.
12. Palmer S, Schildkraut E, Lazarin R, Nguyen J, Nickoloff JA (2003) Gene conversion tracts in Saccharomyces cerevisiae can be extremely short and highly directional. Nucleic Acids Res 31:1164-1173.
13. Schaeffer SW, Anderson WW (2005) Mechanisms of genetic exchange within the chromosomal inversions of Drosophila pseudoobscura. Genetics 171:1729-1739.
14. Hao W (2010) OrgConv: Detection of gene conversion using consensus sequences and its application in plant mitochondrial and chloroplast homologs. BMC Bioinformatics 11:114.
15. Hao W, Palmer JD (2009) Fine-scale mergers of chloroplast and mitochondrial genes create functional, transcompartmentally chimeric mitochondrial genes. Proc Natl Acad Sci USA 106:16728-16733.
16. Mower JP, Stefanovic S, Young GJ, Palmer JD (2004) Plant genetics: Gene transfer from parasitic to host plants. Nature 432:165-166.
17. Mower JP, et al. (2010) Horizontal acquisition of multiple mitochondrial genes from a parasitic plant followed by gene conversion with host mitochondrial genes. BMC Biol, 10.1186/1471-2148-9-265.
18. Schönenberger J, Anderberg AA, Sytsma KJ (2005) Molecular phylogenetics and patterns of floral evolution in the Ericales. Int J Plant Sci 166:265-288.
19. Qiu YL, Palmer JD (2004) Many independent origins of trans splicing of a plant mitochondrial group II intron. J Mol Evol 59:80-89.
20. Janssen T, Bremer K (2004) The age of major monocot groups inferred from 800+ rbcL sequences. Bot J Linn Soc 146:385-398.
21. Bell CD, Soltis DE, Soltis PS (2010) The age and diversification of the angiosperms rerevisited. Am J Bot 97:1296-1303.
22. Shikanai T (2006) RNA editing in plant organelles: Machinery, physiological function and evolution. Cell Mol Life Sci 63:698-708.
23. Mower JP, Touzet P, Gummow JS, Delph LF, Palmer JD (2007) Extensive variation in synonymous substitution rates in mitochondrial genes of seed plants. BMC Evol Biol 7: 135.
24. Adams KL, Qiu YL, Stoutemyer M, Palmer JD (2002) Punctuated evolution of mitochondrial gene content: High and variable rates of mitochondrial gene loss and transfer to the nucleus during angiosperm evolution. Proc Natl Acad Sci USA 99: 9905-9912.
25. Sloan DB, Alverson AJ, Storchová H, Palmer JD, Taylor DR (2010) Extensive loss of translational genes in the structurally dynamic mitochondrial genome of the angiosperm Silene latifolia. BMC Evol Biol 10:274.
26. Cho Y, Qiu YL, Kuhlman P, Palmer JD (1998) Explosive invasion of plant mitochondria by a group I intron. Proc Natl Acad Sci USA 95:14244-14249.
27. Maréchal A, Brisson N (2010) Recombination and the maintenance of plant organelle genome stability. New Phytol 186:299-317.
28. Santoyo G, Martínez-Salazar JM, Rodríguez C, Romero D (2005) Gene conversion tracts associated with crossovers in Rhizobium etli. J Bacteriol 187:4116-4126.
29. Radford SJ, Sabourin MM, McMahan S, Sekelsky J (2007) Meiotic recombination in Drosophila Msh6 mutants yields discontinuous gene conversion tracts. Genetics 176: 53-62.
30. Majewski J, Cohan FM (1999) DNA sequence similarity requirements for interspecific recombination in Bacillus. Genetics 153:1525-1533.
31. Sloan DB, MacQueen AH, Alverson AJ, Palmer JD, Taylor DR (2010) Extensive loss of RNA editing sites in rapidly evolving Silene mitochondrial genomes: Selection vs. retroprocessing as the driving force. Genetics 185:1369-1380.
32. Santoyo G, Romero D (2005) Gene conversion and concerted evolution in bacterial genomes. FEMS Microbiol Rev 29:169-183.
33. Morris RT, Drouin G (2007) Ectopic gene conversions in bacterial genomes. Genome 50:975-984.
34. Baldo L, Bordenstein S, Wernegreen JJ, Werren JH (2006) Widespread recombination throughout Wolbachia genomes. Mol Biol Evol 23:437-449.
35. Chan CX, Beiko RG, Darling AE, Ragan MA (2009) Lateral transfer of genes and gene fragments in prokaryotes. Genome Biol Evol 1:429-438.
36. Edgar RC (2004) MUSCLE: Multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32:1792-1797.
37. Guindon S, Gascuel O (2003) A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 52:696-704.
38. Drummond AJ, Rambaut A (2007) BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol Biol 7:214.
39. Bremer K, Friis EM, Bremer B (2004) Molecular phylogenetic dating of asteroid flowering plants shows early Cretaceous diversification. Syst Biol 53:496-505.
40. Yang Z (2007) PAML 4: Phylogenetic analysis by maximum likelihood. Mol Biol Evol 24:1586-1591.